1972 Laurea in Chimica Industriale, University of Bologna, Italy 1975 Ph.D. in Chemical Physics, University of Southampton (U.K.) 1975-1982 Assistant Professor, University of Bologna 1982-1987 Associate Professor of Physical Chemistry, University of Bologna 1987- Full Professor of Physical Chemistry, Dipartimento di Chimica Fisica ed Inorganica, Faculty of Industrial Chemistry, University of Bologna November 2004-October 2010 - Department Director, Dipartimento di Chimica Fisica ed Inorganica , University of Bologna
Abstract: The prion protein (PrPC) is a glycoprotein that in mammals, differently from avians, can lead to prion diseases, by misfolding into a beta-sheet-rich pathogenic isoform (PrPSc). Mammal and avian proteins show different N-terminal tandem repeats: PHGGGWGQ and PHNPGY, both containing histidine, whereas tyrosine is included only in the primary sequence of the avian protein. Here, by means of potentiometric, circular dichroism (CD), and molecular dynamics (MD) studies at different pH values, we have investigated the conformation of the avian tetrahexarepeat (PHNPGY)(4) (TetraHexaPY) with both N- and C-termini blocked by acetylation and amidation, respectively. We have found, also with the help of a recently proposed protein chirality indicator (Pietropaolo, A.; Muccioli, L.; Berardi, R.; Zannoni, C. Proteins 2008, 70, 667-677), a conformational dependence on the protonation states of histidine and tyrosine residues: the turn formation is pH driven, and at physiological pH a pivotal role is played by the tyrosine OH groups which give rise to a very compact bent structure of backbone upon forming a hydrogen-bond network.
Abstract: We perform large-scale Monte Carlo simulations of orientational ordering in nematic shells and study the type and position of topological defects when an external electric field (homogeneous or quadrupolar) is applied. The field-induced variation of the defect number (and strength) can be used to change the valence of colloidal particles coated with a nematic layer.
Abstract: We perform Monte Carlo simulations of a mixture of soft ellipsoids with embedded quadrupoles as a model of various small molecules dissolved in nematic liquid crystals. We find that Gay-Berne ellipsoids with distributed embedded quadrupoles qualitatively reproduce the trend in the order parameters observed experimentally in NMR spectra. In contrast, ellipsoids with a single embedded quadrupole cannot reproduce the negative order parameter of acetylene in EBBA. (c) 2008 Elsevier B.V. All rights reserved.
Abstract: We present a simple coarse-grained lattice model for monodomain biaxial liquid-crystal elastomers and perform large-scale Monte Carlo simulations in the proposed model system. Orientational ordering --uniaxial or biaxial-- reflects in sample deformations on cooling the system. The simulation output is used to predict calorimetry data and deuterium magnetic resonance spectra.
Abstract: We propose a methodology for the description of the secondary structure of proteins, based on assigning a chirality parameter to short aminoacid sequences according to their arrangement in space at a certain time. We validated the method on ideal and crystalline structures, showing that it can assign secondary structures and that this assignment is robust with respect to random conformational perturbations. From the values of the index and its pattern along a sequence it is possible to recognize many structural motifs of a protein, and in particular poly-L-proline II left-handed helices, often not detected by secondary structure assignment algorithms. Assigning an instantaneous chirality index to the fragments also allows the dynamics to be studied. With this purpose, molecular dynamics simulations were carried out in water for selected hemoglobin (110 ns) and immunoglobulin antigen fragments (50 ns), showing the capability of the chiral index in identifying the stable secondary structure elements, as well as in following their time evolution and conformational changes during the trajectory.
Abstract: We propose a methodology for the realistic simulation and prediction of resonance energy transfer in condensed phases based on a combination of computer simulations of phase morphologies and of a distributed monopole model for the radiationless transfer. The heavy computational demands of the method are moderated by the introduction of a transition charges reduction scheme, originally developed for ground state interactions [Berardi, R. et al. Chem. Phys. Lett. 2004, 389, 373]. We demonstrate the scheme for a condensed glass phase formed by perylene monoimide end-capped 9,9-(di n,n)octvlfluorene trimers, recently studied as light-harvesting materials, where we couple a coarse-grained Monte Carlo Simulation of the molecular organization and a master equation approach modeling the energy diffusion process.
Abstract: We study by means of virtual molecular dynamics computer experiments the response of a bulk biaxial nematic to an applied external field and, in particular, the relative speed of reorientation of the principal director axis and of the secondary one, typical of these new materials, upon a pi/2 field switch. We perform the simulations setting up and integrating the equations of motion for biaxial Gay-Berne particles using quaternions and a suitable time reversible symplectic integrator. We find that switching of the secondary axis is up to an order of magnitude faster than that of the principal axis, and that under fields above a certain strength a reorganization of local domains, temporarily disrupting the nematic and biaxial ordering, rather than a collective concerted reorientation occurs. (c) 2008 American Institute of Physics.
